Delivery mode & infant gut colonization

Mode of delivery is one of the earliest and strongest influences on the infant gut microbiome composition in the first few months of life. Children born by Cesarean section (C-section) lack species from the Bacteroides genus in their gut microbial community, and this difference can be detectable until 6-18 months of age. One hypothesis is that these differences stem from lack of exposure to the maternal vaginal microbiome, as children born by C-section do not pass through the birth canal however, Bacteroides species are not common members of the vaginal microbiome, thus this explanation seems inadequate. Here, we set out to re-evaluate this hypothesis by collecting rectal and vaginal samples before delivery from 75 mothers with paired stool from their infants in the first two weeks of life. We compared microbial profiles of infants born by planned, pre-labor C-section to those born by emergent, post-labor surgery (where the child was in the birth canal, but eventually delivered through an abdominal incision), and found no significant differences in the microbiome between these two groups. Both groups showed the characteristic signature lack of Bacteroides species, despite their difference in exposure to the birth canal. Surprisingly, this signature was only evident in samples from week two of life, but not in the first week. Children born by C-section often had high abundance of Bacteroides in their first few days of life, but these were not stable colonizers of the infant gut, as they were not detectable by week two. Finally, we used metagenomic sequencing to compare microbial strains in maternal vaginal and rectal samples and samples from their infants we found evidence for mother-to-child transmission of rectal rather than vaginal strains. These results challenge birth canal exposure as the dominant factor in infant gut microbiome establishment and implicate colonization efficiency rather than exposure as a dictating factor of the newborn gut microbiome composition.

Classified as human gut / stool / vaginal / urogenital mixed assays of neonate and adult by opus_adjudicated with confidence 0.60. Assay mixed.

• host run.host_tax_id · “9606”
• host study.description · “75 mothers with paired stool from their infants”
• body site study.description · “collecting rectal and vaginal samples before delivery”
• body site study.description · “paired stool from their infants”
• life stage study.description · “infants in the first two weeks of life”
• life stage study.description · “75 mothers”

526 runs over 263 samples · mean 1.07 Gbp per run (median 0.15 Gbp, total 563.18 Gbp; 526 runs with a base count) · layout PAIRED 526 · platform ILLUMINA 526 · models Illumina HiSeq 2000 (263), Illumina MiSeq (263) · 43% of runs with a Sandpiper profile · first public 2020-11-18

Mitchell CM first · Mazzoni C · Hogstrom L · Bryant A · Bergerat A · Cher A · Pochan S · Herman P · Carrigan M · Sharp K · Huttenhower C · Lander ES · Vlamakis H · Xavier RJ · Yassour M last · Zeng S first · Patangia D · Almeida A · Zhou Z · Mu D · Paul Ross R · Stanton C · Wang S last · Li S · Ying J · Wang H · Qu Y · Niu X

PRJNA657818.csv.gz (9.6 KB) · parquet (84.5 KB) — all 263 samples, every field with route and confidence · PRJNA657818_determinations.csv.gz (23.1 KB) — 2,851 evidence rows